tbuckley/cabot-search huggingface dataset:
Goal-seeking compresses neural codes for space in the human hippocampus and orbitofrontal cortex
Authors: Paul S. Muhle-Karbe, Hannah Sheahan, Giovanni Pezzulo, Hugo J. Spiers, Samson Chien, Nicolas W. Schuck, Christopher Summerfield
Journal: Neuron (2023)

Humans can navigate flexibly to meet their goals. Here, we asked how the neural representation of allocentric space is distorted by goal-directed behavior. Participants navigated an agent to two successive goal locations in a grid world environment comprising four interlinked rooms, with a contextual cue indicating the conditional dependence of one goal location on another. Examining the neural geometry by which room and context were encoded in fMRI signals, we found that map-like representations of the environment emerged in both hippocampus and neocortex. Cognitive maps in hippocampus and orbitofrontal cortices were compressed so that locations cued as goals were coded together in neural state space, and these distortions predicted successful learning. This effect was captured by a computational model in which current and prospective locations are jointly encoded in a place code, providing a theory of how goals warp the neural representation of space in macroscopic neural signals.
Advances in the care of breast cancer survivors
Authors: Elizabeth J Cathcart-Rake, Amye J Tevaarwerk, Tufia C Haddad, Stacy D D’Andre, Kathryn J Ruddy
Journal: BMJ (2023)

Abstract Breast cancer survivors may experience significant after effects from diagnoses of breast cancer and cancer directed therapies. This review synthesizes the evidence about optimal management of the sequelae of a diagnosis of breast cancer. It describes the side effects of chemotherapy and endocrine therapy and evidence based strategies for management of such effects, with particular attention to effects of therapies with curative intent. It includes strategies to promote health and wellness among breast cancer survivors, along with data to support the use of integrative oncology strategies. In addition, this review examines models of survivorship care and ways in which digital tools may facilitate communication between clinicians and patients. The strategies outlined in this review are paramount to supporting breast cancer survivors’ quality of life.
Extrinsic and intrinsic preanalytical variables affecting liquid biopsy in cancer
Authors: Syeda Maheen Batool, Tiffaney Hsia, Alexandra Beecroft, Brian Lewis, Emil Ekanayake, Yulia Rosenfeld, Ana K. Escobedo, Austin S. Gamblin, Siddarth Rawal, Richard J. Cote, Mark Watson, David T.W. Wong, Abhijit A. Patel, Johan Skog, Nickolas Papadopoulos, Chetan Bettegowda, Cesar M. Castro, Hakho Lee, Sudhir Srivastava, Bob S. Carter, Leonora Balaj
Journal: Cell Reports Medicine (2023)

Liquid biopsy, through isolation and analysis of disease-specific analytes, has evolved as a promising tool for safe and minimally invasive diagnosis and monitoring of tumors. It also has tremendous utility as a companion diagnostic allowing detection of biomarkers in a range of cancers (lung, breast, colon, ovarian, brain). However, clinical implementation and validation remains a challenge. Among other stages of development, preanalytical variables are critical in influencing the downstream cellular and molecular analysis of different analytes. Although considerable progress has been made to address these challenges, a comprehensive assessment of the impact on diagnostic parameters and consensus on standardized and optimized protocols is still lacking. Here, we summarize and critically evaluate key variables in the preanalytical stage, including study population selection, choice of biofluid, sample handling and collection, processing, and storage. There is an unmet need to develop and implement comprehensive preanalytical guidelines on the optimal practices and methodologies.
How to identify and manage sports related concussions in primary care
Authors: Michael McLarnon, Neil Heron
Journal: BMJ (2023)

Box startWhat you need to know • Concussion rehabilitation should last at least 20 days for non-elite sport participants, with a dedicated relative rest period of 24-48 hours and then phased return to work, education and finally, sport • No return to competitive sport should occur before day 21 following concussion in non-elite athletes • Recovery from concussion varies, but for most people, symptoms will resolve within two weeks.If symptoms have not settled within four weeks, refer patients to a concussion specialist, eg, a consultant in sport and exercise medicine or a neurologist with a specialist interestBox end
Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment
Authors: Xiaoting Xia, Fengwei Zhang, Shuang Li, Xiaoyu Luo, Lixin Peng, Zheng Dong, Hubert Pausch, Alexander S Leonard, Danang Crysnanto, Shikang Wang, Bin Tong, Johannes A Lenstra, Jianlin Han, Fuyong Li, Tieshan Xu, Lihong Gu, Liangliang Jin, Ruihua Dang, Yongzhen Huang, Xianyong Lan, Gang Ren, Yu Wang, Yuanpeng Gao, Zhijie Ma, Haijian Cheng, Yun Ma, Hong Chen, Weijun Pang, Chuzhao Lei, Ningbo Chen
Journal: Genome biology (2023)

Abstract Background Structural variations (SVs) in individual genomes are major determinants of complex traits, including adaptability to environmental variables. The Mongolian and Hainan cattle breeds in East Asia are of taurine and indicine origins that have evolved to adapt to cold and hot environments, respectively. However, few studies have investigated SVs in East Asian cattle genomes and their roles in environmental adaptation, and little is known about adaptively introgressed SVs in East Asian cattle. Results In this study, we examine the roles of SVs in the climate adaptation of these two cattle lineages by generating highly contiguous chromosome-scale genome assemblies. Comparison of the two assemblies along with 18 Mongolian and Hainan cattle genomes obtained by long-read sequencing data provides a catalog of 123,898 nonredundant SVs. Several SVs detected from long reads are in exons of genes associated with epidermal differentiation, skin barrier, and bovine tuberculosis resistance. Functional investigations show that a 108-bp exonic insertion in SPN may affect the uptake of Mycobacterium tuberculosis by macrophages, which might contribute to the low susceptibility of Hainan cattle to bovine tuberculosis. Genotyping of 373 whole genomes from 39 breeds identifies 2610 SVs that are differentiated along a “north–south” gradient in China and overlap with 862 related genes that are enriched in pathways related to environmental adaptation. We identify 1457 Chinese indicine-stratified SVs that possibly originate from banteng and are frequent in Chinese indicine cattle. Conclusions Our findings highlight the unique contribution of SVs in East Asian cattle to environmental adaptation and disease resistance.
Correction: Human CD34+ very small embryonic-like stem cells can give rise to endothelial colony-forming cells with a multistep differentiation strategy using UM171 and nicotinamide acid
Authors: Alison Domingues, Elisa Rossi, Kamila Bujko, Grégoire Detriche, Ulysse Richez, Adeline Blandinieres, Magdalena Kucia, Janina Ratajczak, David M. Smadja, Mariusz Z. Ratajczak
Journal: Leukemia (2023)

Owing to errors introduced during the proofreading process, the label « CB-ECFC » was erroneously added to the Figure .1B and in the legend for panel 1B for the same Fig. 1.This panel shows VSELS-ECFC under different magnification.
Author Correction: Single-cell resolution analysis reveals the preparation for reprogramming the fate of stem cell niche in cotton lateral meristem
Authors: Xiangqian Zhu, Zhongping Xu, Guanying Wang, Yulong Cong, Lu Yu, Ruoyu Jia, Yuan Qin, Guangyu Zhang, Bo Li, Daojun Yuan, Lili Tu, Xiyan Yang, Keith Lindsey, Xianlong Zhang, Shuangxia Jin
Journal: Genome biology (2023)
Author Correction: SARS-CoV-2 reservoir in post-acute sequelae of COVID-19 (PASC)
Authors: Amy D. Proal, Michael B. VanElzakker, Soo Aleman, Katie Bach, Brittany P. Boribong, Marcus Buggert, Sara Cherry, Daniel S. Chertow, Helen E. Davies, Christopher L. Dupont, Steven G. Deeks, William Eimer, E. Wesley Ely, Alessio Fasano, Marcelo Freire, Linda N. Geng, Diane E. Griffin, Timothy J. Henrich, Akiko Iwasaki, David Izquierdo-Garcia, Michela Locci, Saurabh Mehandru, Mark M. Painter, Michael J. Peluso, Etheresia Pretorius, David A. Price, David Putrino, Richard H. Scheuermann, Gene S. Tan, Rudolph E. Tanzi, Henry F. VanBrocklin, Lael M. Yonker, E. John Wherry
Journal: Nature Immunology (2023)
Barriers and facilitators to utilizing digital health technologies by healthcare professionals
Authors: Israel Júnior Borges do Nascimento, Hebatullah Abdulazeem, Lenny Thinagaran Vasanthan, Edson Zangiacomi Martinez, Miriane Lucindo Zucoloto, Lasse Østengaard, Natasha Azzopardi-Muscat, Tomas Zapata, David Novillo-Ortiz
Journal: npj Digital Medicine (2023)

Digital technologies change the healthcare environment, with several studies suggesting barriers and facilitators to using digital interventions by healthcare professionals (HPs). We consolidated the evidence from existing systematic reviews mentioning barriers and facilitators for the use of digital health technologies by HP. Electronic searches were performed in five databases (Cochrane Database of Systematic Reviews, Embase®, Epistemonikos, MEDLINE®, and Scopus) from inception to March 2023. We included reviews that reported barriers or facilitators factors to use technology solutions among HP. We performed data abstraction, methodological assessment, and certainty of the evidence appraisal by at least two authors. Overall, we included 108 reviews involving physicians, pharmacists, and nurses were included. High-quality evidence suggested that infrastructure and technical barriers (Relative Frequency Occurrence [RFO] 6.4% [95% CI 2.9-14.1]), psychological and personal issues (RFO 5.3% [95% CI 2.2-12.7]), and concerns of increasing working hours or workload (RFO 3.9% [95% CI 1.5-10.1]) were common concerns reported by HPs. Likewise, high-quality evidence supports that training/educational programs, multisector incentives, and the perception of technology effectiveness facilitate the adoption of digital technologies by HPs (RFO 3.8% [95% CI 1.8-7.9]). Our findings showed that infrastructure and technical issues, psychological barriers, and workload-related concerns are relevant barriers to comprehensively and holistically adopting digital health technologies by HPs. Conversely, deploying training, evaluating HP's perception of usefulness and willingness to use, and multi-stakeholders incentives are vital enablers to enhance the HP adoption of digital interventions.
Implications for implementation and adoption of telehealth in developing countries: a systematic review of China’s practices and experiences
Authors: Jiancheng Ye, Lu He, Molly Beestrum
Journal: npj Digital Medicine (2023)

Abstract The rapid advancement of telehealth technologies has the potential to revolutionize healthcare delivery, especially in developing countries and resource-limited settings. Telehealth played a vital role during the COVID-19 pandemic, supporting numerous healthcare services. We conducted a systematic review to gain insights into the characteristics, barriers, and successful experiences in implementing telehealth during the COVID-19 pandemic in China, a representative of the developing countries. We also provide insights for other developing countries that face similar challenges to developing and using telehealth during or after the pandemic. This systematic review was conducted through searching five prominent databases including PubMed/MEDLINE, Embase, Scopus, Cochrane Library, and Web of Science. We included studies clearly defining any use of telehealth services in all aspects of health care during the COVID-19 pandemic in China. We mapped the barriers, successful experiences, and recommendations based on the Consolidated Framework for Implementation Research (CFIR). A total of 32 studies met the inclusion criteria. Successfully implementing and adopting telehealth in China during the pandemic necessitates strategic planning across aspects at society level (increasing public awareness and devising appropriate insurance policies), organizational level (training health care professionals, improving workflows, and decentralizing tasks), and technological level (strategic technological infrastructure development and designing inclusive telehealth systems). WeChat, a widely used social networking platform, was the most common platform used for telehealth services. China’s practices in addressing the barriers may provide implications and evidence for other developing countries or low-and middle- income countries (LMICs) to implement and adopt telehealth systems.
Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence
Authors: Shuming Zhang, Long Yuan, Ludmila Danilova, Guanglan Mo, Qingfeng Zhu, Atul Deshpande, Alexander T. F. Bell, Jennifer Elisseeff, Aleksander S. Popel, Robert A. Anders, Elizabeth M. Jaffee, Mark Yarchoan, Elana J. Fertig, Luciane T. Kagohara
Journal: Genome Medicine (2023)

Abstract Background Novel immunotherapy combination therapies have improved outcomes for patients with hepatocellular carcinoma (HCC), but responses are limited to a subset of patients. Little is known about the inter- and intra-tumor heterogeneity in cellular signaling networks within the HCC tumor microenvironment (TME) that underlie responses to modern systemic therapy. Methods We applied spatial transcriptomics (ST) profiling to characterize the tumor microenvironment in HCC resection specimens from a prospective clinical trial of neoadjuvant cabozantinib, a multi-tyrosine kinase inhibitor that primarily blocks VEGF, and nivolumab, a PD-1 inhibitor in which 5 out of 15 patients were found to have a pathologic response at the time of resection. Results ST profiling demonstrated that the TME of responding tumors was enriched for immune cells and cancer-associated fibroblasts (CAF) with pro-inflammatory signaling relative to the non-responders. The enriched cancer-immune interactions in responding tumors are characterized by activation of the PAX5 module, a known regulator of B cell maturation, which colocalized with spots with increased B cell marker expression suggesting strong activity of these cells. HCC-CAF interactions were also enriched in the responding tumors and were associated with extracellular matrix (ECM) remodeling as there was high activation of FOS and JUN in CAFs adjacent to the tumor. The ECM remodeling is consistent with proliferative fibrosis in association with immune-mediated tumor regression. Among the patients with major pathologic responses, a single patient experienced early HCC recurrence. ST analysis of this clinical outlier demonstrated marked tumor heterogeneity, with a distinctive immune-poor tumor region that resembles the non-responding TME across patients and was characterized by HCC-CAF interactions and expression of cancer stem cell markers, potentially mediating early tumor immune escape and recurrence in this patient. Conclusions These data show that responses to modern systemic therapy in HCC are associated with distinctive molecular and cellular landscapes and provide new targets to enhance and prolong responses to systemic therapy in HCC.
Identification of novel genetic risk factors of dilated cardiomyopathy: from canine to human
Authors: Julia E. Niskanen, Åsa Ohlsson, Ingrid Ljungvall, Michaela Drögemüller, Robert F. Ernst, Dennis Dooijes, Hanneke W. M. van Deutekom, J. Peter van Tintelen, Christian J. B. Snijders Blok, Marion van Vugt, Jessica van Setten, Folkert W. Asselbergs, Aleksandra Domanjko Petrič, Milla Salonen, Sruthi Hundi, Matthias Hörtenhuber, Carsten Daub, César L. Araujo, Ileana B. Quintero, Kaisa Kyöstilä, Maria Kaukonen, Meharji Arumilli, Riika Sarviaho, Jenni Puurunen, Sini Sulkama, Sini Karjalainen, Antti Sukura, Pernilla Syrjä, Niina Airas, Henna Pekkarinen, Ilona Kareinen, Hanna-Maaria Javela, Anna Knuuttila, Heli Nordgren, Karoliina Hagner, Tarja Pääkkönen, Antti Iivanainen, Kaarel Krjutskov, Sini Ezer, Auli Saarinen, Shintaro Katayama, Masahito Yoshihara, Abdul Kadir Mukarram, Rasha Fahad Aljelaify, Fiona Ross, Amitha Raman, Irene Stevens, Oleg Gusev, Danika Bannasch, Jeffrey J. Schoenebeck, Juha Kere, W. Glen Pyle, Jonas Donner, Alex V. Postma, Tosso Leeb, Göran Andersson, Marjo K. Hytönen, Jens Häggström, Maria Wiberg, Jana Friederich, Jenny Eberhard, Magdalena Harakalova, Frank G. van Steenbeek, Gerhard Wess, Hannes Lohi
Journal: Genome Medicine (2023)

Abstract Background Dilated cardiomyopathy (DCM) is a life-threatening heart disease and a common cause of heart failure due to systolic dysfunction and subsequent left or biventricular dilatation. A significant number of cases have a genetic etiology; however, as a complex disease, the exact genetic risk factors are largely unknown, and many patients remain without a molecular diagnosis. Methods We performed GWAS followed by whole-genome, transcriptome, and immunohistochemical analyses in a spontaneously occurring canine model of DCM. Canine gene discovery was followed up in three human DCM cohorts. Results Our results revealed two independent additive loci associated with the typical DCM phenotype comprising left ventricular systolic dysfunction and dilatation. We highlight two novel candidate genes, RNF207 and PRKAA2 , known for their involvement in cardiac action potentials, energy homeostasis, and morphology. We further illustrate the distinct genetic etiologies underlying the typical DCM phenotype and ventricular premature contractions. Finally, we followed up on the canine discoveries in human DCM patients and discovered candidate variants in our two novel genes. Conclusions Collectively, our study yields insight into the molecular pathophysiology of DCM and provides a large animal model for preclinical studies.
Disparities in spatially variable gene calling highlight the need for benchmarking spatial transcriptomics methods
Authors: Natalie Charitakis, Agus Salim, Adam T. Piers, Kevin I. Watt, Enzo R. Porrello, David A. Elliott, Mirana Ramialison
Journal: Genome biology (2023)

Identifying spatially variable genes (SVGs) is a key step in the analysis of spatially resolved transcriptomics data. SVGs provide biological insights by defining transcriptomic differences within tissues, which was previously unachievable using RNA-sequencing technologies. However, the increasing number of published tools designed to define SVG sets currently lack benchmarking methods to accurately assess performance. This study compares results of 6 purpose-built packages for SVG identification across 9 public and 5 simulated datasets and highlights discrepancies between results. Additional tools for generation of simulated data and development of benchmarking methods are required to improve methods for identifying SVGs.
Experts consensus on the procedure of dental operative microscope in endodontics and operative dentistry
Authors: Bin Liu, Xuedong Zhou, Lin Yue, Benxiang Hou, Qing Yu, Bing Fan, Xi Wei, Lihong Qiu, Zhengwei Huang, Wenwei Xia, Zhe Sun, Hanguo Wang, Liuyan Meng, Bin Peng, Chen Zhang, Shuli Deng, Zhaojie Lu, Deqin Yang, Tiezhou Hou, Qianzhou Jiang, Xiaoli Xie, Xuejun Liu, Jiyao Li, Zuhua Wang, Haipeng Lyu, Ming Xue, Jiuyu Ge, Yi Du, Jin Zhao, Jingping Liang
Journal: International Journal of Oral Science (2023)

Abstract The dental operative microscope has been widely employed in the field of dentistry, particularly in endodontics and operative dentistry, resulting in significant advancements in the effectiveness of root canal therapy, endodontic surgery, and dental restoration. However, the improper use of this microscope continues to be common in clinical settings, primarily due to operators’ insufficient understanding and proficiency in both the features and established operating procedures of this equipment. In October 2019, Professor Jingping Liang, Vice Chairman of the Society of Cariology and Endodontology, Chinese Stomatological Association, organized a consensus meeting with Chinese experts in endodontics and operative dentistry. The objective of this meeting was to establish a standard operation procedure for the dental operative microscope. Subsequently, a consensus was reached and officially issued. Over the span of about four years, the content of this consensus has been further developed and improved through practical experience.
Endocrine aspects of metabolic dysfunction-associated steatotic liver disease (MASLD): Beyond insulin resistance
Authors: Alan L. Hutchison, Federica Tavaglione, Stefano Romeo, Michael Charlton
Journal: Journal of Hepatology (2023)

While the links between metabolic dysfunction associated steatotic liver disease liver disease (MASLD) and obesity, insulin resistance are widely appreciated, there are a host of complex interactions between the liver and other endocrine axes. While it can be difficult to definitively distinguish direct causal relationships and those attributable to increased adipocyte mass, there is substantial evidence of direct and indirect specific endocrine dysregulation and severity of MASLD. Strong evidence of direct and indirect effects exists for low levels of growth hormone, sex hormones, and thyroid hormone with development and severity of disease. The impact of steroid hormones, e.g. cortisol and dehydropepiandrosterone, and adipokines is much more divergent. Thoughtful assessment, based on individual risk factors and findings, and also of management of non-insulin endocrine axes should be performed in the evaluation and management of MASLD. Multiple therapeutic pharmaceutical targets have emerged that leverage various endocrine axes to reduce the fibroinflammatory cascade in metabolic dysfunction associated steatohepatitis (MASH).
Incidence of sexual violence among recently arrived asylum-seeking women in France: a retrospective cohort study
Authors: Jérémy Khouani, Marion Landrin, Rachel Cohen Boulakia, Sarah Tahtah, Gaëtan Gentile, Anne Desrues, Marine Vengeon, Anderson Loundou, Adriaan Barbaroux, Pascal Auquier, Maeva Jego
Journal: The Lancet Regional Health - Europe (2023)

The prevention of sexual violence (SV) occurring shortly after arrival in host countries towards female asylum seekers requires knowledge about its incidence. We aimed to determine the incidence of SV and its associated factors during the past year of living in France among asylum-seeking females who had arrived more than one year earlier but less than two years.We conducted a retrospective cohort study using a life-event survey of asylum-seeking females who had been registered in southern France by the Office for Immigration for more than one year but less than two. The primary outcome was the occurrence of SV during the past year, weighted by the deviation in age and geographical origin of our sample from all females registered. The nature of SV was noted, and associated factors were explored by a logistic regression model.Between October 1, 2021, and March 31, 2022, 273 females were included. Eighty-four females experienced SV during the past year of living in France (26.3% weighted [95% CI, 24-28.8]), 17 of whom were raped (4.8% weighted [95% CI, 3.7-6.1]). Being a victim of SV prior to arrival in France (202, 75.7%) was associated with the occurrence of SV after arrival (OR = 4.6 [95% CI, 1.8-11.3]). Lack of support for accommodation was associated with se.xual assault (OR = 2.6 [95% CI, 1.3-5.1]).The months following arrival in a European host country among asylum-seeking females appear to be a period of high incidence of SV; even higher for those who previously experienced SV prior to arrival. Reception conditions without support for accommodation seem to increase exposure to sexual assault.DGOS-GIRCI.